I've been looking at gear sets for my Dana 30 front and Dana 44 rear. I find that a 4.09 is available for one, and a 4.10 the other in many cases. Can you use a 4.09 on one end and a 4.10 on the other without ill-effects?

Manufacturers really don't do anything...it has to do with the size of the R&P. Different diffs have different sizes of ring gears and pinion heads and that comes through in the gear ratio. Anything within a 1% difference isn't anything to worry about (general rule of thumb).

actually it's normal because the 4.09 gears are 11 teeth on the pinion 45 on the ring and 4.11 gears are 10 pinion/ 41 ring.
fords were notorious for this because the 9" gears were different than dana gears. 4.09/4.11 is way close enough.

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I install gears!
lots of gears
gears that make you go, gears that make you slow.